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Shao B, Wang Y, Zhang J, Wang Y, Tan J, Wang L, Hu P, Tan J, Xu Z. Mutation spectrum of thalassemia among pre-pregnant adults in the Jiangsu Province by capillary electrophoresis-based multiplex PCR assay. Mol Genet Genomic Med 2024; 12:e2344. [PMID: 38112059 PMCID: PMC10767610 DOI: 10.1002/mgg3.2344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 11/02/2023] [Accepted: 12/07/2023] [Indexed: 12/20/2023] Open
Abstract
BACKGROUND Thalassemia is a common genetic disorder in southwestern China, and an increasing number of cases from eastern China have been recently reported. Here, we developed a rapid, convenient, and accurate assay to evaluate the mutation spectrum of thalassemia in eastern China. METHODS A carrier screening assay for 61 hotspot variants among HBA1/HBA2 and HBB (OMIM: 141800, 141850, and 141900) genes was developed by SNaPshot/high-throughput ligation-dependent probe amplification (HLPA) technology. We used this assay to detect the mutation spectrum of thalassemia in individuals from eastern China and compared with the data collected from literatures focused on southern and northern China for variant distribution. RESULTS Among 4276 tested individuals, 2.62% (112/4276) were α-thalassemia carriers, with 90 carrying one deletion or mutation and 22 carrying two deletions. 0.40% (17/4276) were β-thalassemia carriers, and the most common variant of β-thalassemia was c.126_129delCTTT (29.41%) followed by c.316-197C>T (23.53%). The genotype distribution in our study was similar to those from southern China populations. CONCLUSION The Chinese population from different regions presented comparable mutation spectrum of thalassemia, and the SNaPshot/HLPA technique may serve as a capable assay for a routine genetic test in clinical practice with its accurate, rapid, and inexpensive advantage.
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Affiliation(s)
- Binbin Shao
- Department of Prenatal DiagnosisWomen's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care HospitalNanjingPeople's Republic of China
| | - Yuguo Wang
- Department of Prenatal DiagnosisWomen's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care HospitalNanjingPeople's Republic of China
| | - Jingjing Zhang
- Department of Prenatal DiagnosisWomen's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care HospitalNanjingPeople's Republic of China
| | - Yan Wang
- Department of Prenatal DiagnosisWomen's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care HospitalNanjingPeople's Republic of China
| | - Juan Tan
- Department of Prenatal DiagnosisWomen's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care HospitalNanjingPeople's Republic of China
| | - Lulu Wang
- Department of Prenatal DiagnosisWomen's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care HospitalNanjingPeople's Republic of China
| | - Ping Hu
- Department of Prenatal DiagnosisWomen's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care HospitalNanjingPeople's Republic of China
| | - Jianxin Tan
- Department of Prenatal DiagnosisWomen's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care HospitalNanjingPeople's Republic of China
| | - Zhengfeng Xu
- Department of Prenatal DiagnosisWomen's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care HospitalNanjingPeople's Republic of China
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Rahmani N, Ahmadvand M, Khakpour G. Use of expanded carrier screening for retrospective diagnosis of two deceased siblings with Van Maldergem syndrome 2: case report. ASIAN BIOMED 2022; 16:322-328. [PMID: 37551355 PMCID: PMC10392142 DOI: 10.2478/abm-2022-0036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/09/2023]
Abstract
Van Maldergem syndrome (VMLDS) is a recessive disease which affects multiple organs including the face, ear, and limb extremities. It can be caused by pathogenic variants in either the gene DCHS1 or FAT4. Diagnosis of VMLDS is complicated, especially regarding its similarity of symptoms to Hennekam syndrome, another disorder caused by FAT4 variants. Reported patients are two infantile siblings with multiple congenital anomalies, who deceased without clinical diagnosis. Whole exome sequencing was exploited for expanded carrier screening (ECS) of their parents, which revealed a novel splicing variant in the gene FAT4, NM_024582.6: c.7018+1G>A. In silico analysis of the variant indicates loss of canonical donor splice site of intron 6. This variant is classified as pathogenic based on ACMG criteria. Reverse phenotyping of patients resulted in likely diagnosis of VMLDS2. This study reaffirms the possibility of using ECS, leading to the genetic diagnosis of a rare disease with complicated clinical features.
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Affiliation(s)
- Nasim Rahmani
- Department of Medical Genetics and Molecular Biology, School of Medicine, Iran University of Medical Sciences, Tehran1449614535, Iran
| | - Mohammad Ahmadvand
- Department of Oncology and Stem Cell Transplantation, Shariati Hospital, School of Medicine, Tehran University of Medical Sciences, Tehran1411713135, Iran
| | - Golnaz Khakpour
- Department of Medical Genetics and Molecular Biology, School of Medicine, Iran University of Medical Sciences, Tehran1449614535, Iran
- Department of Eye Research Center, The Five Senses Institute, Rassoul Akram Hospital, School of Medicine, Iran University of Medical Sciences, Tehran1445613131, Iran
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3
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A capillary electrophoresis-based multiplex PCR assay for expanded carrier screening in the eastern Han Chinese population. NPJ Genom Med 2022; 7:6. [PMID: 35079019 PMCID: PMC8789796 DOI: 10.1038/s41525-021-00280-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 12/20/2021] [Indexed: 12/05/2022] Open
Abstract
Expanded carrier screening, a type of reproductive genetic testing for couples, has gained tremendous popularity for assessing the risk of passing on certain genetic conditions to offspring. Here, a carrier screening assay for 448 pathogenic variants was developed using capillary electrophoresis-based multiplex PCR technology. The capillary electrophoresis-based multiplex PCR assay achieved a sensitivity, specificity, and accuracy of 97.4%, 100%, and 99.6%, respectively, in detecting the specific variants. Among the 1915 couples (3830 individuals), 708 individuals (18.5%) were identified as carriers for at least one condition. Of the 708 carriers, 633 (89.4%) were heterozygous for one condition, 71 (10.0%) for two disorders, 3 (0.4%) for three disorders, and 1 (0.1%) for four disorders. Meanwhile, 30 (1.57%) couples were identified as at‐risk couples. This study describes an inexpensive and effective method for expanded carrier screening. The simplicity and accuracy of this approach will facilitate the clinical implementation of expanded carrier screening.
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Yamada M, Suzuki H, Shima T, Uehara T, Kosaki K. A patient with compound heterozygosity of SMPD4: Another example of utility of exome-based copy number analysis in autosomal recessive disorders. Am J Med Genet A 2021; 188:613-617. [PMID: 34622574 DOI: 10.1002/ajmg.a.62535] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 09/25/2021] [Indexed: 11/11/2022]
Abstract
For the efficient diagnosis of rare and undiagnosed diseases, the parallel detection of copy number variants (CNVs) and single nucleotide variants using exome analysis is required. Recently, our group reported the usefulness of a program called EXCAVATOR2, which screens for CNVs from aligned exome data in bam format. This method is expected to contribute to the identification of structural variants and to improve the diagnosis rate, especially for the diagnosis of autosomal recessive disease, when a conventional exome analysis identifies a pathogenic variant in one allele but not the other. Here we report a 2-year-old Japanese boy with an undiagnosed disease. He had severe neonatal asphyxia, severe intellectual disability, intractable seizures, cerebellar and brainstem hypoplasia and dysmorphic features including a prominent supraorbital ridge, thin upper lip, and prominent antihelix. An exome analysis reinforced with a copy number analysis using the EXCAVATOR2 method revealed that the patient had a hemizygous variant in chr2(GRCh37):g.130925108G>A, NM_017951.4 c.832C>T, p.(Arg278*) in SMPD4 that was derived from his father and a deletion of SMPD4 derived from his mother. The presence of the deletion spanning SMPD4 was confirmed by short-read and long-read whole-genome sequencing. The successful diagnosis of this reported patient demonstrates the diagnostic utility of EXCAVATOR2 and overcomes the weakness of exome analysis for the detection of autosomal recessive diseases in nonconsanguineous families, significantly impacting genetic counseling for family planning.
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Affiliation(s)
- Mamiko Yamada
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Hisato Suzuki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Taiki Shima
- Department of Pediatrics, Juntendo University Urayasu Hospital, Chiba, Japan
| | - Tomoko Uehara
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan.,Department of Pediatrics, Central Hospital, Aichi Developmental Disability Center, Aichi, Japan
| | - Kenjiro Kosaki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
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Peluso F, Caraffi SG, Zuntini R, Trimarchi G, Ivanovski I, Valeri L, Barbieri V, Marinelli M, Pancaldi A, Melli N, Cesario C, Agolini E, Cellini E, Radio FC, Crisafi A, Napoli M, Guerrini R, Tartaglia M, Novelli A, Gargano G, Zuffardi O, Garavelli L. Whole Exome Sequencing Is the Minimal Technological Approach in Probands Born to Consanguineous Couples. Genes (Basel) 2021; 12:genes12070962. [PMID: 34202629 PMCID: PMC8303193 DOI: 10.3390/genes12070962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/19/2021] [Accepted: 06/21/2021] [Indexed: 11/30/2022] Open
Abstract
We report on two siblings suffering from different pathogenic conditions, born to consanguineous parents. A multigene panel for brain malformations and microcephaly identified the homozygous splicing variant NM_005886.3:c.1416+1del in the KATNB1 gene in the older sister. On the other hand, exome sequencing revealed the homozygous frameshift variant NM_005245.4:c.9729del in the FAT1 gene in the younger sister, who had a more complex phenotype: in addition to bilateral anophthalmia and heart defects, she showed a right split foot with 4 toes, 5 metacarpals, second toe duplication and preaxial polydactyly on the right hand. These features have been never reported before in patients with pathogenic FAT1 variants and support the role of this gene in the development of limb buds. Notably, each parent was heterozygous for both of these variants, which were ultra-rare and rare, respectively. This study raises awareness about the value of using whole exome/genome sequencing rather than targeted gene panels when testing affected offspring born to consanguineous couples. In this way, exomic data from the parents are also made available for carrier screening, to identify heterozygous pathogenetic and likely pathogenetic variants in genes responsible for other recessive conditions, which may pose a risk for subsequent pregnancies.
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Affiliation(s)
- Francesca Peluso
- Medical Genetics Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy; (F.P.); (S.G.C.); (R.Z.); (G.T.); (I.I.); (L.V.); (V.B.); (M.M.)
| | - Stefano Giuseppe Caraffi
- Medical Genetics Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy; (F.P.); (S.G.C.); (R.Z.); (G.T.); (I.I.); (L.V.); (V.B.); (M.M.)
| | - Roberta Zuntini
- Medical Genetics Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy; (F.P.); (S.G.C.); (R.Z.); (G.T.); (I.I.); (L.V.); (V.B.); (M.M.)
| | - Gabriele Trimarchi
- Medical Genetics Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy; (F.P.); (S.G.C.); (R.Z.); (G.T.); (I.I.); (L.V.); (V.B.); (M.M.)
| | - Ivan Ivanovski
- Medical Genetics Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy; (F.P.); (S.G.C.); (R.Z.); (G.T.); (I.I.); (L.V.); (V.B.); (M.M.)
- Institut für Medizinische Genetik, Universität Zürich, 8952 Zürich, Switzerland
| | - Lara Valeri
- Medical Genetics Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy; (F.P.); (S.G.C.); (R.Z.); (G.T.); (I.I.); (L.V.); (V.B.); (M.M.)
- Post Graduate School of Paediatrics, University of Modena and Reggio Emilia, 41124 Modena, Italy;
| | - Veronica Barbieri
- Medical Genetics Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy; (F.P.); (S.G.C.); (R.Z.); (G.T.); (I.I.); (L.V.); (V.B.); (M.M.)
| | - Maria Marinelli
- Medical Genetics Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy; (F.P.); (S.G.C.); (R.Z.); (G.T.); (I.I.); (L.V.); (V.B.); (M.M.)
| | - Alessia Pancaldi
- Post Graduate School of Paediatrics, University of Modena and Reggio Emilia, 41124 Modena, Italy;
- Neonatal Intensive Care Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy; (N.M.); (G.G.)
| | - Nives Melli
- Neonatal Intensive Care Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy; (N.M.); (G.G.)
| | - Claudia Cesario
- Translational Cytogenomics Research Unit, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy; (C.C.); (E.A.); (A.N.)
| | - Emanuele Agolini
- Translational Cytogenomics Research Unit, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy; (C.C.); (E.A.); (A.N.)
| | - Elena Cellini
- Pediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Meyer Children’s Hospital, University of Florence, 50139 Florence, Italy; (E.C.); (R.G.)
| | - Francesca Clementina Radio
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00165 Rome, Italy; (F.C.R.); (M.T.)
| | - Antonella Crisafi
- Pediatric Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy;
| | - Manuela Napoli
- Neuroradiology Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy;
| | - Renzo Guerrini
- Pediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Meyer Children’s Hospital, University of Florence, 50139 Florence, Italy; (E.C.); (R.G.)
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00165 Rome, Italy; (F.C.R.); (M.T.)
| | - Antonio Novelli
- Translational Cytogenomics Research Unit, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy; (C.C.); (E.A.); (A.N.)
| | - Giancarlo Gargano
- Neonatal Intensive Care Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy; (N.M.); (G.G.)
| | - Orsetta Zuffardi
- Unit of Medical Genetics, Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy;
| | - Livia Garavelli
- Medical Genetics Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy; (F.P.); (S.G.C.); (R.Z.); (G.T.); (I.I.); (L.V.); (V.B.); (M.M.)
- Correspondence:
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Präimplantationsdiagnostik für monogene Erkrankungen am PID-Zentrum Regensburg. MED GENET-BERLIN 2019. [DOI: 10.1007/s11825-019-00263-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Zusammenfassung
Wir berichten über die Erfahrungen unseres PID-Zentrums bei der Präimplantationsdiagnostik (PID) für 149 Familien mit hohem Risiko für eine monogene Erkrankung bei den Nachkommen und die Ergebnisse aus 316 PID-Zyklen. Seit 2001 wurden bei uns insgesamt 251 Diagnostikzyklen mittels Polkörperdiagnostik (PKD) durchgeführt. Nach der Zulassung unserer Gruppe als PID-Zentrum im Juni 2015 haben wir inzwischen für 45 Familien insgesamt 65 Trophektoderm-Diagnostikzyklen (TED) nach Trophektoderm (TE)-Biopsie durchgeführt (1,4/Familie). Unsere vorläufigen Daten bestätigen eine hohe Diagnoseeffizienz beider Verfahren mit Verdopplung der klinischen Schwangerschaftsrate pro Transfer nach TED auf 48,2 % verglichen mit 22,9 % nach PKD. Bei einer durchschnittlichen Rate von 4,3 verfügbaren Blastozysten pro TED-Zyklus ist die Rate von Zyklen ohne transferierbare Embryonen mit 27,7 % (für 6/45 Familien = 13,3 %) erwartungsgemäß höher als bei der PKD (14,7 %) für durchschnittlich 8 Eizellen pro Zyklus mit erfolgreicher Biopsie beider Polkörper. Schon mit dem ersten Transfer konnte jedoch nach TED für 55,3 % der Paare eine klinische Schwangerschaft erreicht werden. Insgesamt ermöglichte die TED kumulativ nach durchschnittlich 1,4 Transferen eine klinische Schwangerschaft für 68,5 % der Familien mit Transfer und insgesamt eine schonendere Behandlung mit weniger TED-Zyklen (PKD: kumulativ 40,3 % nach 2,3 Transferen), weniger Hormonstimulationen und entsprechend auch geringeren Kosten. Insbesondere die Subgruppe der weiblichen Überträgerinnen von Repeaterkrankungen mit insgesamt niedrigeren Erfolgschancen scheint nach unseren vorläufigen Daten von der TED zu profitieren.
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Liu Z, Zhu L, Roberts R, Tong W. Toward Clinical Implementation of Next-Generation Sequencing-Based Genetic Testing in Rare Diseases: Where Are We? Trends Genet 2019; 35:852-867. [PMID: 31623871 DOI: 10.1016/j.tig.2019.08.006] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 08/08/2019] [Accepted: 08/28/2019] [Indexed: 02/07/2023]
Abstract
Next-generation sequencing (NGS) technologies have changed the landscape of genetic testing in rare diseases. However, the rapid evolution of NGS technologies has outpaced its clinical adoption. Here, we re-evaluate the critical steps in the clinical application of NGS-based genetic testing from an informatics perspective. We suggest a 'fit-for-purpose' triage of current NGS technologies. We also point out potential shortcomings in the clinical management of genetic variants and offer ideas for potential improvement. We specifically emphasize the importance of ensuring the accuracy and reproducibility of NGS-based genetic testing in the context of rare disease diagnosis. We highlight the role of artificial intelligence (AI) in enhancing understanding and prioritization of variance in the clinical setting and propose deep learning frameworks for further investigation.
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Affiliation(s)
- Zhichao Liu
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA.
| | - Liyuan Zhu
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA
| | - Ruth Roberts
- ApconiX, Alderley Park, Alderley Edge, SK10 4TG, UK; University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Weida Tong
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA.
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Wheway G, Mitchison HM. Opportunities and Challenges for Molecular Understanding of Ciliopathies-The 100,000 Genomes Project. Front Genet 2019; 10:127. [PMID: 30915099 PMCID: PMC6421331 DOI: 10.3389/fgene.2019.00127] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 02/05/2019] [Indexed: 01/11/2023] Open
Abstract
Cilia are highly specialized cellular organelles that serve multiple functions in human development and health. Their central importance in the body is demonstrated by the occurrence of a diverse range of developmental disorders that arise from defects of cilia structure and function, caused by a range of different inherited mutations found in more than 150 different genes. Genetic analysis has rapidly advanced our understanding of the cell biological basis of ciliopathies over the past two decades, with more recent technological advances in genomics rapidly accelerating this progress. The 100,000 Genomes Project was launched in 2012 in the UK to improve diagnosis and future care for individuals affected by rare diseases like ciliopathies, through whole genome sequencing (WGS). In this review we discuss the potential promise and medical impact of WGS for ciliopathies and report on current progress of the 100,000 Genomes Project, reviewing the medical, technical and ethical challenges and opportunities that new, large scale initiatives such as this can offer.
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Affiliation(s)
- Gabrielle Wheway
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, United Kingdom
| | - Hannah M. Mitchison
- Genetics and Genomic Medicine, University College London, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
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